1. The lack of Neanderthal mtDNA is easy to explain. Neanderthal mom’s had kids who ended up in Neanderthal tribes and their descendants died out with the Neanderthals. Only hybrid kids with modern human mothers and hence modern human mtDNA ended up in modern human tribes that survived in the long run.
It could be that modern humans got Neanderthal women pregnant as often as Neanderthals got modern human women pregnant. Indeed a few hybrid Neanderthals could help explain the advance in Neanderthal tool culture near the very end of the Neanderthal era after hundreds of thousands of years of relative stagnation, despite the apparent absence in the archeological record of mixed Neanderthal-human communities.
But, unless Neanderthal-modern human liasons were long term stable relationships as opposed to brief sexual episodes between neighboring groups that had little to do with each other and didn’t actually marry, the children are always going to end up in the mother’s tribe nine months later (give or take, who knows if Neanderthal gestation was precisely the same in length). Even affairs of a few months in length while a Neanderthal and modern human tribe were near each other for a season, for example, wouldn’t prevent the child from ending up in the mother’s tribe.
2. Haldane’s law is the best way to explain the lack of Neanderthal Y-DNA (hybrids tend strongly to have the same sex determination chromosome). Another possibility is that the Neanderthals were more sex dimorphic than modern humans, so hybrid boys may have been more different from the modern human norm than hybrid girls, and hence may have integrated less well and had more trouble finding mates.
3. Random drift to explain the lack of Neanderthal mtDNA and Y-DNA doesn’t fit well with an estimated 197-430 liasons. The law of averages iterated that many times in an expanding modern human population would catch up with you to keep mtDNA and Y-DNA in the population at similar rates to other autosomal traces otherwise.
You need a scenario that acts very soon (within a couple of generations) to purge both mtDNA and Y-DNA, and very consistently, when you have hundreds of liasons to keep all Neanderthal mtDNA and Y-DNA out of the Eurasian gene pool. Declining and stable populations jettison low frequency genes. But expanding populations that have the same genes repeatedly reinjected into their gene pools generally don’t nearly as easily. And, it is hard to explain introgression that occurs time and time again leaving no Y-DNA or mtDNA in circumstances that still somehow leave some siginificant traces (on the order of 2%) in the autosomal genome that can reach fixation, without some causal reason that Y-DNA and mtDNA behave differently.
4. There are some skeletons from the Upper Paleolithic in Europe that seem to show possibly hybrid individuals or Neanderthal weighted traits in modern humans, suggesting that there may really have been some more admixed modern humans.
5. If modern admixture is based on nearly 10,000 years of liasons spaced evenly during periods when the two species are in contact with each other at the frontier, it is virtually impossible not to end up with some cline of greater admixture in Europe than the rest of the world, since any admixture that took place in Europe itself after 50kya surely would have made its way into European gene pools but would not have made its way in any measurable way to coastal route Asia. More opportunities for liasons means more admixture even if only incrementally.
A better way to explain this is that on the frontiers modern humans were more admixed with Neanderthals through successive liasons, but that a very small percentage of modern humans in Europe trace ancestry to European Cro-Mags with high levels of admixture on that frontier from 30kya. Instead, most Europeans trace their ancestors mostly to post-Neanderthal extinction people from less admixed areas to the Southeast – partially in the post-LGM repopulation of Europe and partially in the Neolithic and in possible later waves of migration (e.g. Indo-European) to the extent that they had demographic impact.
It is realistic to expect that modern Europeans have less (perhaps much less) than 5% pre-LGM European Cro-Mag ancestry on average, which is diluted enough to make even 10%-20% Neanderthal admixture rates in final frontier European Cro-Mags disappear to undetectable levels.
6. This said, an estimate of one admixture event in the proto-Eurasian modern human community per generation during the period of admixture in the Southwest and West Asian area for the period of interspecies contact prior to a meaningful modern human presence in Europe sounds about right as a ballpark estimate from back of napkin estimates without having to resort to very low fertility rates.
Even within modern humans, differences between, for example, Chadic pastoralists and Fulani pastoralists are great enough to keep the Y-DNA pools of the two neighboring groups in the African Sahel extremely distinct from each other over periods of thousands of years. Neanderthals and modern humans can be expected to have had lower admixture rates than any two neighboring modern human populations known to history and not separated by significant geographic barriers. Surely, admixture rates would have been at least as low as between high caste South Asians and Dalits over the last 4,500 years or so, simply out of social factors and with no fertility effects.
7. Even if you are going to posit that liasons were much more common, infanticide seems a more likely source of limited Neanderthal contribution than extremely low fertility, if we assume that Upper Paleolithic humans were no more “civilized” than e.g. the Romans were. In general, however, no low fertility rate estimate can address the fact that admixture is just as high in Asians as it is in Europeans despite a presumably shorter period of contact with Neanderthals for their ancestors.
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